Lyme disease is the most common arthropod-borne infection in the United States. Over 100,000 cases have been reported to date. The disease is a multisystem disorder with dermatologic, neurologic and rheumatologic manifestations. Borrelia burgdorferi, the causative agent of Lyme disease, alternates between the microenvironments of the tick vector and a mammalian host. When Borrelia burgdorferi is transmitted from the tick vector to the mammalian host, the bacterium experiences significant alterations in temperature and pH. Previously, we observed numerous alterations in the membrane protein profile when B. burgdorferi B31 was grown at pH 7.0 compared to pH 8.0. We have subsequently identified ten genes localizing to linear plasmids that are regulated by the pH in vitro. Seven genes were indirectly identified by Matrix Assisted Laser Ionization Desorption Time of Flight(MALDI-TOF) analysis of proteins separated by 2D-NEPHGE that were synthesized in greater amounts when spirochetes were grown at pH 7.0 versus pH 8.0. Another gene was identified by screening a B. burgdorferi B31 genomic library with cross-adsorbed hyperimmune rabbit serum. Two additional genes were identified by Northern blot analysis. All ten genes were transcriptionally regulated, yet the degree of pH regulation observed in cultures grown at pH 7.0 compared to pH 8.0 varied, where some genes were more tightly regulated than others. The regulation of genes in response to the change in pH may aid B. burgdorferi in adapting effectively to either the tick or the mammalian environment.